Glass material isn't transparent when looked through another glass material?
This appears to be because of overlapping faces. That is, two faces being in the same position. I cannot guarantee this is the case, but two transmission materials overtop of eachother sounds fragile.
I recommend either scaling the liquid block down slightly, or doing the following to change the liquid setup:
Make the separate liquid object just the surface.
Change the underwater part of the glass to a liquid-colored material that has a refraction index so as to match light going from glass into water as opposed to leaving air. You could probably get away with subtracting the IOR of glass from that of water, then adding 1. For a more accurate result, I'd have to think about the math, here's the law: https://en.wikipedia.org/wiki/Snell%27s_law If you aren't sure what to do, I might could look into it.
Hope this helps :D